**************************************************************************** File name: 9gxh.pdb no. of DNA/RNA chains: 2 [C=15,D=15] no. of nucleotides: 30 no. of atoms: 2668 no. of waters: 345 no. of metals: 3 [K=3] **************************************************************************** List of 17 base pairs nt1 nt2 bp name Saenger LW DSSR 1 C.DG1 C.DG6 G+G -- 06-VI cWH cW+M 2 C.DG1 C.DG15 G+G -- 06-VI cHW cM+W 3 C.DG2 C.DG5 G+G -- 06-VI cHW cM+W 4 C.DG2 C.DG14 G+G -- 06-VI cWH cW+M 5 C.DG5 C.DG11 G+G -- 06-VI cHW cM+W 6 C.DG6 C.DG10 G+G -- 06-VI cWH cW+M 7 C.DG10 C.DG15 G+G -- 06-VI cWH cW+M 8 C.DG11 C.DG14 G+G -- 06-VI cHW cM+W 9 D.DG1 D.DG6 G+G -- 06-VI cWH cW+M 10 D.DG1 D.DG15 G+G -- 06-VI cHW cM+W 11 D.DG2 D.DG5 G+G -- 06-VI cHW cM+W 12 D.DG2 D.DG14 G+G -- 06-VI cWH cW+M 13 D.DG5 D.DG11 G+G -- 06-VI cHW cM+W 14 D.DG6 D.DG10 G+G -- 06-VI cWH cW+M 15 D.DG8 D.DT9 G+T Platform -- cSH cm+M 16 D.DG10 D.DG15 G+G -- 06-VI cWH cW+M 17 D.DG11 D.DG14 G+G -- 06-VI cHW cM+W **************************************************************************** List of 4 multiplets 1 nts=4 GGGG C.DG1,C.DG6,C.DG10,C.DG15 2 nts=4 GGGG C.DG2,C.DG5,C.DG11,C.DG14 3 nts=4 GGGG D.DG1,D.DG6,D.DG10,D.DG15 4 nts=4 GGGG D.DG2,D.DG5,D.DG11,D.DG14 **************************************************************************** List of 4 helices Note: A helix is defined by base-stacking interactions, regardless of pair type and backbone connectivity, and may contain more than one stem. helix#number[stems-contained] bps=number-of-base-pairs in the helix bp-type: '|' for a canonical WC/wobble pair, '.' otherwise helix-form: classification of a dinucleotide step comprising the bp above the given designation and the bp that follows it. Types include 'A', 'B' or 'Z' for the common A-, B- and Z-form helices, '.' for an unclassified step, and 'x' for a step without a continuous backbone. -------------------------------------------------------------------- helix#1[0] bps=2 strand-1 5'-GG-3' bp-type .. strand-2 3'-GG-5' helix-form . 1 C.DG1 C.DG6 G+G -- 06-VI cWH cW+M 2 C.DG2 C.DG5 G+G -- 06-VI cHW cM+W -------------------------------------------------------------------------- helix#2[0] bps=2 strand-1 5'-GG-3' bp-type .. strand-2 3'-GG-5' helix-form . 1 C.DG10 C.DG15 G+G -- 06-VI cWH cW+M 2 C.DG11 C.DG14 G+G -- 06-VI cHW cM+W -------------------------------------------------------------------------- helix#3[0] bps=2 strand-1 5'-GG-3' bp-type .. strand-2 3'-GG-5' helix-form . 1 D.DG5 D.DG11 G+G -- 06-VI cHW cM+W 2 D.DG6 D.DG10 G+G -- 06-VI cWH cW+M -------------------------------------------------------------------------- helix#4[0] bps=3 strand-1 5'-GGG-3' bp-type ... strand-2 3'-TGG-5' helix-form x. 1 D.DG8 D.DT9 G+T Platform -- cSH cm+M 2 D.DG1 D.DG15 G+G -- 06-VI cHW cM+W 3 D.DG2 D.DG14 G+G -- 06-VI cWH cW+M **************************************************************************** List of 10 base stacks Note: A stack is an ordered list of nucleotides assembled together via base-stacking interactions, regardless of backbone connectivity. Stacking interactions within a stem are *not* included. 1 nts=2 QT B.GLN44,D.DT7 2 nts=2 GG C.DG5,C.DG6 3 nts=3 RTW A.ARG52,D.DT12,B.TRP47 4 nts=3 RGG B.ARG45,D.DG5,D.DG6 5 nts=3 TGG C.DT9,C.DG15,C.DG14 6 nts=3 GGT C.DG10,C.DG11,C.DT13 7 nts=3 TGG D.DT9,D.DG15,D.DG14 8 nts=4 YTGG B.TYR37,D.DT13,D.DG11,D.DG10 9 nts=4 TGGG C.DT4,C.DG2,C.DG1,C.DG8 10 nts=5 WTGGG B.TRP105,D.DT4,D.DG2,D.DG1,D.DG8 **************************************************************************** Nucleotides not involved in stacking interactions nts=4 TTTT C.DT3,C.DT7,C.DT12,D.DT3 **************************************************************************** List of 2 atom-base capping interactions dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 sugar O4'@C.DG8 C.DG6 2.67 2 sugar O4'@D.DG8 D.DG6 2.65 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=15 GGTTGGTGTGGTTGG C.DG1,C.DG2,C.DT3,C.DT4,C.DG5,C.DG6,C.DT7,C.DG8,C.DT9,C.DG10,C.DG11,C.DT12,C.DT13,C.DG14,C.DG15 2 nts=15 GGTTGGTGTGGTTGG D.DG1,D.DG2,D.DT3,D.DT4,D.DG5,D.DG6,D.DT7,D.DG8,D.DT9,D.DG10,D.DG11,D.DT12,D.DT13,D.DG14,D.DG15 **************************************************************************** List of 4 G-tetrads 1 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.331 type=bowl nts=4 GGGG C.DG1,C.DG15,C.DG10,C.DG6 2 glyco-bond=-s-s sugar=.--- groove=wnwn planarity=0.249 type=bowl-2 nts=4 GGGG C.DG2,C.DG14,C.DG11,C.DG5 3 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.305 type=other nts=4 GGGG D.DG1,D.DG15,D.DG10,D.DG6 4 glyco-bond=-s-s sugar=.--- groove=wnwn planarity=0.211 type=other nts=4 GGGG D.DG2,D.DG14,D.DG11,D.DG5 **************************************************************************** List of 2 G4-helices Note: a G4-helix is defined by stacking interactions of G4-tetrads, regardless of backbone connectivity, and may contain more than one G4-stem. helix#1[1] stems=[#1] layers=2 INTRA-molecular 1 glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG C.DG1,C.DG15,C.DG10,C.DG6 2 glyco-bond=-s-s sugar=.--- groove=wnwn WC-->Major nts=4 GGGG C.DG2,C.DG14,C.DG11,C.DG5 step#1 mm(<>,outward) area=17.98 rise=3.51 twist=13.2 strand#1 DNA glyco-bond=s- sugar=-. nts=2 GG C.DG1,C.DG2 strand#2 DNA glyco-bond=-s sugar=-- nts=2 GG C.DG15,C.DG14 strand#3 DNA glyco-bond=s- sugar=-- nts=2 GG C.DG10,C.DG11 strand#4 DNA glyco-bond=-s sugar=-- nts=2 GG C.DG6,C.DG5 -------------------------------------------------------------------------- helix#2[1] stems=[#2] layers=2 INTRA-molecular 1 glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG D.DG1,D.DG15,D.DG10,D.DG6 2 glyco-bond=-s-s sugar=.--- groove=wnwn WC-->Major nts=4 GGGG D.DG2,D.DG14,D.DG11,D.DG5 step#1 mm(<>,outward) area=16.85 rise=3.51 twist=14.0 strand#1 DNA glyco-bond=s- sugar=-. nts=2 GG D.DG1,D.DG2 strand#2 DNA glyco-bond=-s sugar=-- nts=2 GG D.DG15,D.DG14 strand#3 DNA glyco-bond=s- sugar=-- nts=2 GG D.DG10,D.DG11 strand#4 DNA glyco-bond=-s sugar=-- nts=2 GG D.DG6,D.DG5 **************************************************************************** List of 2 G4-stems Note: a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along each of the four strands. stem#1[#1] layers=2 INTRA-molecular loops=3 descriptor=2(+Ln+Lw+Ln) note=2+2 UDUD anti-parallel:chair 1 glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG C.DG1,C.DG15,C.DG10,C.DG6 2 glyco-bond=-s-s sugar=.--- groove=wnwn WC-->Major nts=4 GGGG C.DG2,C.DG14,C.DG11,C.DG5 step#1 mm(<>,outward) area=17.98 rise=3.51 twist=13.2 strand#1 U DNA glyco-bond=s- sugar=-. nts=2 GG C.DG1,C.DG2 strand#2 D DNA glyco-bond=-s sugar=-- nts=2 GG C.DG15,C.DG14 strand#3 U DNA glyco-bond=s- sugar=-- nts=2 GG C.DG10,C.DG11 strand#4 D DNA glyco-bond=-s sugar=-- nts=2 GG C.DG6,C.DG5 loop#1 type=lateral strands=[#1,#4] nts=2 TT C.DT3,C.DT4 loop#2 type=lateral strands=[#4,#3] nts=3 TGT C.DT7,C.DG8,C.DT9 loop#3 type=lateral strands=[#3,#2] nts=2 TT C.DT12,C.DT13 -------------------------------------------------------------------------- stem#2[#1] layers=2 INTRA-molecular loops=3 descriptor=2(+Ln+Lw+Ln) note=2+2 UDUD anti-parallel:chair 1 glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG D.DG1,D.DG15,D.DG10,D.DG6 2 glyco-bond=-s-s sugar=.--- groove=wnwn WC-->Major nts=4 GGGG D.DG2,D.DG14,D.DG11,D.DG5 step#1 mm(<>,outward) area=16.85 rise=3.51 twist=14.0 strand#1 U DNA glyco-bond=s- sugar=-. nts=2 GG D.DG1,D.DG2 strand#2 D DNA glyco-bond=-s sugar=-- nts=2 GG D.DG15,D.DG14 strand#3 U DNA glyco-bond=s- sugar=-- nts=2 GG D.DG10,D.DG11 strand#4 D DNA glyco-bond=-s sugar=-- nts=2 GG D.DG6,D.DG5 loop#1 type=lateral strands=[#1,#4] nts=2 TT D.DT3,D.DT4 loop#2 type=lateral strands=[#4,#3] nts=3 TGT D.DT7,D.DG8,D.DT9 loop#3 type=lateral strands=[#3,#2] nts=2 TT D.DT12,D.DT13 **************************************************************************** List of 7 splayed-apart dinucleotides 1 C.DG6 C.DT7 angle=85 distance=12.9 ratio=0.68 2 C.DT7 C.DG8 angle=144 distance=18.1 ratio=0.95 3 C.DG11 C.DT12 angle=140 distance=17.0 ratio=0.94 4 C.DT12 C.DT13 angle=139 distance=17.5 ratio=0.94 5 D.DT7 D.DG8 angle=149 distance=18.6 ratio=0.96 6 D.DG11 D.DT12 angle=132 distance=17.8 ratio=0.91 7 D.DT12 D.DT13 angle=140 distance=17.8 ratio=0.94 ---------------------------------------------------------------- Summary of 4 splayed-apart units 1 nts=3 GTG C.DG6,C.DT7,C.DG8 2 nts=3 GTT C.DG11,C.DT12,C.DT13 3 nts=2 TG D.DT7,D.DG8 4 nts=3 GTT D.DG11,D.DT12,D.DT13 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >9gxh nts=30 [whole] GGTTGGTGTGGTTGG&GGTTGGTGTGGTTGG ...............&............... >9gxh-C #1 nts=15 0.73(2.56) [chain] DNA GGTTGGTGTGGTTGG ............... >9gxh-D #2 nts=15 0.73(2.45) [chain] DNA GGTTGGTGTGGTTGG ............... **************************************************************************** Summary of structural features of 30 nucleotides Note: the first five columns are: (1) serial number, (2) one-letter shorthand name, (3) dbn, (4) id string, (5) rmsd (~zero) of base ring atoms fitted against those in a standard base reference frame. The sixth (last) column contains a comma-separated list of features whose meanings are mostly self-explanatory, except for: turn: angle C1'(i-1)--C1'(i)--C1'(i+1) < 90 degrees break: no backbone linkage between O3'(i-1) and P(i) 1 G . C.DG1 0.005 syn,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad 2 G . C.DG2 0.010 anti,BI,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad 3 T . C.DT3 0.009 turn,anti,~C3'-endo,BI,non-stack,ss-non-loop 4 T . C.DT4 0.007 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 5 G . C.DG5 0.009 syn,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad 6 G . C.DG6 0.011 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad,cap-acceptor,splayed-apart 7 T . C.DT7 0.007 turn,anti,~C2'-endo,non-stack,ss-non-loop,splayed-apart 8 G . C.DG8 0.010 anti,~C3'-endo,non-pair-contact,ss-non-loop,cap-donor,splayed-apart 9 T . C.DT9 0.007 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate 10 G . C.DG10 0.010 syn,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad 11 G . C.DG11 0.011 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad,splayed-apart 12 T . C.DT12 0.007 turn,syn,~C2'-endo,BII,non-stack,ss-non-loop,splayed-apart 13 T . C.DT13 0.010 anti,~C2'-endo,BII,non-pair-contact,ss-non-loop,splayed-apart 14 G . C.DG14 0.012 syn,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad 15 G . C.DG15 0.008 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad 16 G . D.DG1 0.014 syn,~C2'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 17 G . D.DG2 0.010 anti,BI,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad 18 T . D.DT3 0.007 turn,anti,~C3'-endo,BI,non-stack,ss-non-loop 19 T . D.DT4 0.006 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 20 G . D.DG5 0.012 syn,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad,phosphate 21 G . D.DG6 0.007 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad,cap-acceptor 22 T . D.DT7 0.009 turn,anti,~C2'-endo,ss-non-loop,splayed-apart 23 G . D.DG8 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,ss-non-loop,cap-donor,splayed-apart 24 T . D.DT9 0.007 turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,ss-non-loop 25 G . D.DG10 0.009 syn,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad 26 G . D.DG11 0.008 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad,phosphate,splayed-apart 27 T . D.DT12 0.008 turn,anti,~C3'-endo,BII,ss-non-loop,phosphate,splayed-apart 28 T . D.DT13 0.009 anti,~C2'-endo,BII,non-pair-contact,ss-non-loop,phosphate,splayed-apart 29 G . D.DG14 0.010 syn,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad 30 G . D.DG15 0.013 anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad **************************************************************************** List of 14 additional files 1 dssr-pairs.pdb -- an ensemble of base pairs 2 dssr-multiplets.pdb -- an ensemble of multiplets 3 dssr-helices.pdb -- an ensemble of helices (coaxial stacking) 4 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 5 dssr-2ndstrs.ct -- secondary structure in connectivity table format 6 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 7 dssr-torsions.txt -- backbone torsion angles and suite names 8 dssr-splays.pdb -- an ensemble of splayed-apart units 9 dssr-stacks.pdb -- an ensemble of base stacks 10 dssr-atom2bases.pdb -- an ensemble of atom-base stacking interactions 11 dssr-rotmat.txt -- position vector and rotation matrix 12 dssr-viewV.pdb -- vertical view of the principal moment of inertia 13 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 14 dssr-viewT.pdb -- top view of the principal moment of inertia